A micro-channel device includes one or more micro (sub-millimeter) channels through which one or more small volumes of samples are routed for processing and/or analysis. An example of such a device includes a biochip, a lab-on-a-chip, and/or other micro-channel device. An application in which a micro-channel device has been used is DNA sequencing. DNA sequencing generally is a method for determining an order of nucleotide bases (adenine, guanine, cytosine, and thymine) of DNA in a sample of DNA.
For DNA sequencing, the DNA in the sample is lysed, producing fragments of sequences of the four nucleotides. The fragments are replicated through polymerase chain reaction (PCR) and labeled with target specific fluorescent dyes (e.g., one for each nucleotide base), each dye having a different spectral emission characteristic (e.g., wavelength, frequency, energy and color). The labeled fragments are separated by size through electrophoresis. The DNA fragments are sequenced based on the spectral characteristics of the dyes. This has included using an optical detection system to illuminate the fragments with an excitation signal and detecting the fluoresced radiation of the dyes. The detected spectral information is used to identify the nucleotides and sequence the DNA.
A micro-channel location identification routine is performed on the micro-channel device before the fragment reaches the optical reading region for processing. This information is subsequently used by the optical detection system to focus the excitation signal at the fragments in the device and correlate a detected signal with the corresponding channel. One approach to identifying the location of the micro-channels has been based on a level of a detected reflected excitation signal. An example of this is shown in FIG. 1. In FIG. 1, photodiode (PD) 102 and (PD) 104 are located on opposing sides of a micro-channel device 106, which includes a plurality of micro-channels 108. The micro-channel device 106 is scanned by an excitation signal 112 with a focal spot 114 at a depth corresponding to a height of a center region 116 of the channels 108, and the photodiodes 102 and 104 detect reflected excitation signals 110.
The level of the detected reflected excitation signal 110 depends on a material composition of the region of the micro-channel device 106 illuminated by the excitation signal 112. This is shown in FIGS. 2, 3, 4 and 5. In FIG. 2, the focal spot 114 of the excitation signal 112 is in a bulk material region 202 of the micro-channel device 106 where little to none of the excitation signal 112 is reflected. As a consequence, the level of any reflected signal detected by the photodiodes 102 and 104, and hence their respective outputs, is relatively small. In FIG. 3, the focal spot 114 of the excitation signal 112 is in a non-material region 302 of a micro-channel 108 of the micro-channel device 106 where little to none of the excitation signal 112 is reflected. Likewise, the level of any reflected signal detected by the photodiodes 102 and 104, and hence their respective outputs, is relatively small.
In FIG. 4, the focal spot 114 is on a bulk material region/non-material region interface 402 on the photodiode 102 side of the micro-channel 108, and a portion of the excitation signal 112 is reflected through the micro-channel 108 towards the photodiode 104, which detects the deflected excitation signal 110. In FIG. 5, the focal spot 114 is on a bulk material region/non-material region interface 502 on the photodiode 104 side of the micro-channel 108, and a portion of the excitation signal 112 is reflected through the micro-channel 108 towards the photodiode 102. In this instance, the photodiodes 102 and 104 detect the reflected excitation signal, and generate output signals having amplitudes indicative of the levels of the detected reflected signals.
From FIGS. 2-5, the level of the deflected excitation signal 110 detected by and the amplitude of the signal output by the photodiodes 102 and 104 is indicative the region of the micro-channel device 106 illuminated by the excitation signal 112. As such, with this approach, the excitation signal 112 is scanned across the micro-channel device 106, and the amplitude of the signal output by the photodiodes 102 and 104 is recorded and mapped to the scan position of the excitation signal 112 on the micro-channel device 106. The micro-channels 108 are located in the micro-channel device 106 based on the peaks or maximums in the recorded signals, which correspond to the interfaces 402 and 502, which correspond to the edges of the micro-channels 108. The locations of the micro-channels 108 are then used by the optical detection system to focus the excitation signal 112 at the samples for processing.
Unfortunately, the above approach requires additional hardware (i.e., the photodiodes 102 and 104), and this additional hardware may increase overall optical detection system cost, complexity and/or footprint. Furthermore, the optical detection system also has to additionally be configured to process the signals output by the photodiodes 102 and 104.